Recent Publications
1. Fast Epistasis Detection in Large-Scale GWAS for Intel Xeon Phi Clusters, Glenn Luecke, Nathan Weeks, Brandon Groth, Marina Kraeva, Li Ma, Like Kramer, James Koltes, James Reecy, PBio 2015: Third International Workshop on Parallelism in Bioinformatics. August 20-22, 2015, Helsinki, Finland. See http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7345653 This is a high-quality conference with papers carefully reviewed.
2. “High Performance Epistasis Detection in Quantitative Trait GWAS” Luecke et al, submitted to International Journal of High Performance Computing. January 2016 revising based on referee comments. This is a high quality journal where all papers are carefully reviewed.
3. Weeks, Nathan T.; Luecke, Glenn R.; Groth, Brandon M.; Kraeva, Marina; Ma, Li; Kramer, Luke M., Koltes, James E.; Reecy, James M. "High Performance Epistasis Detection in Quantitative Trait GWAS". International Journal of High Performance Computing, vol. doi:10.1177/1094342016658110. July 2016. All papers are reviewed with most not being accepted.
4. Weeks, Nathan T.; Luecke, Glenn R. "Performance Analysis and Optimization of SAMtools Sorting". European Conference on Parallel Processing, August 2016. All papers are carefully reviewed with most being rejected
5. “Researchers use Edison to Improve Performance, Energy Efficiency of Bioinformatics Application”, National Energy Research Supercomputing Center (NERSC) Science News, September 13, 2016. It is an honor that our research was featured in NERCS News and we accepted their request.
6. Luecke, Brandon Groth, Nathan Weeks, Marina Kraeva, “Comparing Allinea’s and Intel’s Performance Tools for HPC”, High Performance Computing Symposium, Virginia Beach, Virginia, April 2017. (High-quality conference and challenging to get a paper accepted due to a strong refereeing process.)
7. “The Performance and Scalability of the SHMEM and corresponding MPI-3 Routines on a Cray XC30” with Gianina Alina Negoita, Glenn Luecke, Marina Kraeva, Gurpur Prabhu, and James P. Vary. ISPDC-2017: The 16th International Symposium on Parallel and
Distributed Computing, 3-6 July 2017, Innsbruck, Austria. Refereed paper in a high-quality conference with all papers carefully reviewed. The following is the official listing:
\bibitem{SHMEM2017} G. A. Negoita, G. R. Luecke, M. Kraeva, G. M. Prabhu, and J. P. Vary. The performance and scalability of the SHMEM and corresponding MPI routines on a Cray XC30. In: {\it Proceedings of the 16^{th} International Symposium on Parallel and Distributed Computing (ISPDC 2017)}. July 3–6, 2017, Innsbruck, Austria. {\it IEEE}, Jul. 2017, pp. 62–69, ISBN: 978-1-5386-0862-3, DOI: 10.1109/ISPDC.2017.19 It will be published on http://ieeeexplore.ieee.org
8. “Optimization of SAMtools Sorting Using OpenMP Tasks”, Luecke and Weeks, Cluster Computing. Volume 20 Number 2, 2017. (high-quality, refereed journal)
9. “Accelerating MPI Reductions on Intel Xeon Phi”, Nathan Weeks, Glenn Luecke, Piter Maris, James Vary, refereed poster for EuroMPI, Chicago, September 2017. The poster can be found at https://iastate.box.com/v/posterljsoijf and the extended abstract at
https://iastate.box.com/v/abstractowije
10. “HPC-Bench: A Tool to Optimize HPC Benchmarking Workflow”. Gianina Alina Negoita, Glenn Luecke, Shashi Gadia, This is a refereed poster presented at the Supercomputing 2017 conference in Denver, Colorado, November 12, 2017.
11. “HPC-Bench: A Tool to Optimize HPC Benchmarking Workflow”, Gianina Alina Negoita, Glenn Luecke, Shashi Gadia, Published in the Computational Tools conference proceedings, February, 2018. ISSN: 2308-4170 ISBN: 978-1-61208-613-2, see
http://www.thinkmind.org/index.php?view=article&articleid=computation_tools_2018_1_20_80009 (Remember all papers are refereed including this paper.)
12. “Deep Learning: A Tool for Computational Nuclear Physics”, Gianina Alina Negoita, Glenn Luecke, James Vary, etc. Published in the Computational Tools conference proceedings, February 18, 2018, pp 18-22. ISSN: 2308-4170 ISBN: 978-1-61208-613-2, see
http://www.thinkmind.org/index.php?view=article&articleid=computation_tools_2018_1_40_80017 (Remember all papers are refereed including this paper.) RECEIVED THE BEST PAPER AWARD! See: https://crd.lbl.gov/news-and-publications/news/2018/berkeley-lab-resear…
13. “Using Machine Learning to Improve Shared-Memory General Matrix-Matrix Multiplication”, Brandon Groth and Glenn R. Luecke, International Conference on Parallel and Distributed Processing Technologies and Applications (lPDPTA 2018, pp 128 – 131, Las Vegas, August 2018. Refereed papers only in this conference.
14. “Challenges Developing MPI Fault-Tolerant Fortran Applications” Nathan Weeks, Glenn R. Luecke, James Vary, Pieter Maris, IEEE Cluster 2018, Belfast, UK, September 2018, pp 524-531 All papers are refereed. doi: 10.1109/CLUSTER.2018.00068
15. G. A. Negoita, J. P. Vary, G. R. Luecke, P. Maris, A. M. Shirokov, I. K. Shin, Y. Kim, E. G. Ng, C. Yang, M. Lockner, and G. M. Prabhu, “Deep Learning: Extrapolation Tool for Ab Initio Nuclear Theory”, Phys. Rev. C 99, 054308 (2019), DOI: 10.1103/PhysRevC.99.054308; arXiv:1810.04009 [nucl-th]